pypi: Scaffold | Projects | Ecosyste.ms: Papers

10.1155/2013/581862

iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections
Cited by: 62
Author(s): Hung V. Trinh, Jonas Grossmann, Peter Gehrig, Bernd Roschitzki, Ralph Schlapbach, Urs F. Greber, Silvio Hemmi
Software Mentions: 2
Published: over 13 years ago

10.1128/mBio.02146-17

A Phosphorylation Switch on Lon Protease Regulates Bacterial Type III Secretion System in Host
Cited by: 23
Author(s): Xiaofeng Zhou, Doron Teper, Maxuel O. Andrade, Tong Zhang, Sixue Chen, Wenlei Song, Nian Wang
Software Mentions: 2
Published: over 8 years ago

10.1038/s41398-020-00966-4

Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218
Cited by: 9
Author(s): Magdalena Jurkiewicz, Dirk Moser, Antonius Koller, Lei Yu, Emily I. Chen, David A. Bennett, Turhan Canli
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.01096-18

Migration of Type III Secretion System Transcriptional Regulators Links Gene Expression to Secretion
Cited by: 9
Author(s): Spyridoula N. Charova, Anastasia D. Gazi, Efstratios Mylonas, Charalambos Pozidis, Blanca Sabarit, D. Anagnostou, Konstantina Psatha, Michalis Aivaliotis, Carmen R. Beuzón, Nickolas J. Panopoulos, Michael Kokkinidis
Software Mentions: 2
Published: about 8 years ago

10.7150/thno.47893

Analysis of mesenchymal stem cell proteomes <i>in situ</i> in the ischemic heart
Cited by: 11
Author(s): Dunzheng Han, Junjie Yang, Eric Zhang, Yanwen Liu, Chan Boriboun, Aijun Qiao, Yang Yu, Shuyuan Xu, Yang Liu, Wenying Yan, Biao Luo, Dagang Lü, Chunxiang Zhang, Chunfa Jie, James A. Mobley, Jianyi Zhang, Gangjian Qin
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-021-95060-0

Proteomic study of Desulfovibrio ferrophilus IS5 reveals overexpressed extracellular multi-heme cytochrome associated with severe microbiologically influenced corrosion
Cited by: 9
Author(s): Mohor Chatterjee, Yu Fan, Fang Cao, A. A. Jones, Giovanni Pilloni, Xiaozhou Zhang
Software Mentions: 2
Published: about 5 years ago

10.3390/toxins8040105

Quantitative Proteomic Analysis of Venoms from Russian Vipers of Pelias Group: Phospholipases A2 are the Main Venom Components
Cited by: 29
Author(s): Sergey I. Kovalchuk, Rustam H. Ziganshin, Vladislav G. Starkov, Victor I. Tsetlin, Yuri N. Utkin
Software Mentions: 2
Published: over 10 years ago

10.1128/mBio.01137-19

Identification of Extracellular DNA-Binding Proteins in the Biofilm Matrix
Cited by: 89
Author(s): J.S. Kavanaugh, Caralyn E. Flack, Jessica Lister, Erica B. Ricker, Carolyn B. Ibberson, Christian Jenul, Derek E. Moormeier, Elizabeth Delmain, Kenneth W. Bayles, Alexander R. Horswill
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4890-8

A high-density genetic map of extra-long staple cotton (Gossypium barbadense) constructed using genotyping-by-sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line population
Cited by: 24
Author(s): Fan Lü, Liping Wang, Xinyi Wang, Haiyan Zhang, Yanfei Zhu, Jiayan Guo, Wenwei Gao, Hao Geng, Quanjia Chen, Yanying Qu
Software Mentions: 2
Published: over 8 years ago

10.1186/s12915-017-0439-6

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)
Cited by: 54
Author(s): Peter A. Larsen, R. Alan Harris, Yue Liu, Shwetha C. Murali, C. Ryan Campbell, Adam D. Brown, Beth A. Sullivan, Jennifer Shelton, Susan J. Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C. Durand, Muhammad S. Shamim, E Aiden, Donna M. Muzny, Richard A. Gibbs, Anne D. Yoder, Jeffrey Rogers, Kim C. Worley
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-021-86284-1

Ibuprofen alters epoxide hydrolase activity and epoxy-oxylipin metabolites associated with different metabolic pathways in murine livers
Cited by: 4
Author(s): Shuchita Tiwari, Jun Yang, Christophe Morisseau, Blythe Durbin‐Johnson, Bruce D. Hammock, Aldrin V. Gomes
Software Mentions: 2
Published: over 5 years ago

10.3934/Neuroscience.2019.4.299

Brain proteomics links oxidative stress with metabolic and cellular stress response proteins in behavioural alteration of Alzheimer’s disease model rats
Cited by: 3
Author(s): Mohammad Azizur Rahman, Shahdat Hossain, Noorlidah Abdullah, Norhaniza Aminudin
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-020-79545-y

Surface hydrophobics mediate functional dimerization of CYP121A1 of Mycobacterium tuberculosis
Cited by: 5
Author(s): Amit Kumar, Christopher S. Campomizzi, Natalie Jay, Shaun Ferguson, Emelie‐Jo Scheffler, James Lioi, Chengjian Tu, Jun Qu, Claire Simons, D. Fernando Estrada
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-76052-y

Human perinatal stem cell derived extracellular matrix enables rapid maturation of hiPSC-CM structural and functional phenotypes
Cited by: 21
Author(s): Travis J. Block, Jeffery Creech, A.M. Rocha, Milos Marinkovic, Daniela Ponce-Balbuena, Eric N. Jiménez-Vázquez, Sy Griffey, Todd J. Herron
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-91756-5

Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives
Cited by: 4
Author(s): Mana Iwata, Ana Gutiérrez, Gisela Marques, Grzegorz Sabat, Philip J. Kersten, Daniel Cullen, Jennifer M. Bhatnagar, J. S. Yadav, Anna Lipzen, Yuko Yoshinaga, Aarti Sharma, Catherine Adam, Christopher Daum, Vivian Ng, Igor V. Grigoriev, Chiaki Hori
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-66286-1

A new brilliantly blue-emitting luciferin-luciferase system from Orfelia fultoni and Keroplatinae (Diptera)
Cited by: 16
Author(s): Vadim R. Viviani, Jaqueline R. Silva, Danilo T. Amaral, Vanessa R. Bevilaqua, Fábio Camargo Abdalla, Bruce R. Branchini, Carl Hirschie Johnson
Software Mentions: 2
Published: over 6 years ago

10.1126/sciadv.aba8397

The structures of natively assembled clathrin-coated vesicles
Cited by: 38
Author(s): Mohammadreza Paraan, Joshua H. Mendez, Savanna R. Sharum, Danielle L. Kurtin, Huan He, Scott M. Stagg
Software Mentions: 2
Published: about 6 years ago

10.1038/sdata.2015.22

Proteomic analysis of colon and rectal carcinoma using standard and customized databases
Cited by: 21
Author(s): Robbert J.C. Slebos, Xia Wang, Xiaojing Wang, Bing Zhang, David L. Tabb, Daniel C. Liebler
Software Mentions: 2
Published: over 11 years ago

10.1016/j.redox.2019.101265

Oxygen-dependent bond formation with FIH regulates the activity of the client protein OTUB1
Cited by: 13
Author(s): Christina Pickel, Julia Günter, Amalia Ruiz-Serrano, Patrick Spielmann, Jacqueline-Alba Fabrizio, Witold Wolski, Daniel J. Peet, Roland H. Wenger, Carsten C. Scholz
Software Mentions: 2
Published: about 7 years ago

10.1098/rsos.181433

Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses
Cited by: 9
Author(s): Elena R. Schroeter, Kevin Blackburn, Michael B. Goshe, Mary H. Schweitzer
Software Mentions: 2
Published: about 7 years ago

10.1016/j.xpro.2021.100417

Identifying cytokine signaling signatures in primary human Th-1 cells by phospho-proteomics analysis
Cited by: 0
Author(s): Jonathan Martínez-Fábregas, Elizabeth Pöhler, Ignacio Moraga
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-68985-1

A benzimidazole inhibitor attenuates sterile inflammation induced in a model of systemic autoinflammation in female mice
Cited by: 4
Author(s): Federica Agliano, Keaton Karlinsey, Michael Ragazzi, Antoine Ménoret, Anthony T. Vella
Software Mentions: 2
Published: about 6 years ago

10.3390/proteomes7010010

Comparative Proteomic Analysis Unveils Critical Pathways Underlying the Role of Nitrogen Fertilizer Treatment in American Elderberry
Cited by: 1
Author(s): Bo Yang, Andrew L. Thomas, C. Michael Greenlief
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1009506

The antiviral sirtuin 3 bridges protein acetylation to mitochondrial integrity and metabolism during human cytomegalovirus infection
Cited by: 16
Author(s): Xuanyu Sheng, Ileana M. Cristea
Software Mentions: 2
Published: over 5 years ago

10.3390/proteomes7020014

Extracellular Vesicle Integrins Distinguish Unique Cancers
Cited by: 43
Author(s): Stephanie N. Hurwitz, David G. Meckes
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1008086

Nedd8 hydrolysis by UCH proteases in Plasmodium parasites
Cited by: 16
Author(s): Maryia Karpiyevich, Sophie H. Adjalley, Marco Mol, David B. Ascher, Bethany Mason, Gerbrand J. van der Heden van Noort, Heike Laman, Huib Ovaa, Marcus Lee, Katerina Artavanis‐Tsakonas
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13068-018-1350-2

Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles
Cited by: 19
Author(s): Jiaxi Miao, Mengmeng Wang, Lei Ma, Tuo Li, Qiwei Huang, Dongyang Liu, Qirong Shen
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1003830

Lysine Acetyltransferase GCN5b Interacts with AP2 Factors and Is Required for Toxoplasma gondii Proliferation
Cited by: 61
Author(s): Jiachen Wang, Stacy E. Dixon, Li Min Ting, Ting-Kai Liu, Victoria Jeffers, Matthew McKnight Croken, Myrasol Calloway, Dominique Cannella, Mohamed‐Ali Hakimi, Kami Kim, William J. Sullivan
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.ppat.1008307

An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing
Cited by: 7
Author(s): Raymond Wong, Ahalya Balachandran, Peter K. Cheung, Ran Cheng, Qun Pan, Peter Stoilov, P. Richard Harrigan, Benjamin J. Blencowe, Donald R. Branch, Alan Cochrane
Software Mentions: 2
Published: over 6 years ago

10.3390/proteomes8030014

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field
Cited by: 133
Author(s): Emmalyn J. Dupree, Madhuri Jayathirtha, Hannah Yorkey, Marius Mihăşan, Brîndușa Alina Petre, Costel C. Darie
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-70010-4

The AAA + ATPase valosin-containing protein (VCP)/p97/Cdc48 interaction network in Leishmania
Cited by: 3
Author(s): Bruno Aguiar, Carole Dumas, Halim Maaroufi, Prasad K. Padmanabhan, Barbara Papadopoulou
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.00603-21

Toxoplasma gondii Matrix Antigen 1 Is a Secreted Immunomodulatory Effector
Cited by: 14
Author(s): Tadakimi Tomita, Debanjan Mukhopadhyay, Bing Han, Rama R. Yakubu, Vincent Tu, Joshua Mayoral, Tatsuki Sugi, Yanfen Ma, Jeroen P. J. Saeij, Louis M. Weiss
Software Mentions: 2
Published: over 5 years ago

10.1172/JCI86924

Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques
Cited by: 108
Author(s): Sarah R. Langley, Karin Willeit, Athanasios Didangelos, Ljubica Matic, Philipp Skroblin, Javier Barallobre-Barreiro, Mariette Lengquist, Gregor Rungger, Alexander Kapustin, Ludmilla Kedenko, Chris Molenaar, Ruifang Lu, Temo Barwari, Gonca Suna, Xiaoke Yin, Bernhard Iglseder, Bernhard Paulweber, Peter Willeit, Joseph Shalhoub, Gérard Pasterkamp, Alun H. Davies, Claudia Monaco, Ulf Hedin, Catherine M. Shanahan, Johann Willeit, Stefan Kiechl, Manuel Mayr
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-9-595

Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species
Cited by: 53
Author(s): Hernán Lorenzi, Mathangi Thiagarajan, Brian J. Haas, Jennifer Wortman, Neil Hall, Elisabet Caler
Software Mentions: 2
Published: almost 18 years ago

10.14814/phy2.12035

Clathrin complexes with the inhibitor kappa B kinase signalosome: imaging the interactome
Cited by: 5
Author(s): Fabia Gamboni, Guillermo A. Escobar, Ernest E. Moore, Monika Dzieciątkowska, Kirk C. Hansen, Sanchayita Mitra, Trevor A. Nydam, Christopher C. Silliman, Anirban Banerjee
Software Mentions: 2
Published: over 12 years ago

10.1016/j.jbc.2021.100912

Cryo-EM reveals conformational flexibility in apo DNA polymerase ζ
Cited by: 4
Author(s): Chloe D. Truong, Theodore A. Craig, Gaofeng Cui, Maria Victoria Botuyan, Rachel A. Serkasevich, Kayi Y. Chan, Georges Mer, Po-Lin Chiu, Rajiv Kumar
Software Mentions: 2
Published: about 5 years ago

10.1242/jcs.154880

Tyrosine phosphorylation of WIP releases bound WASP and impairs podosome assembly in macrophages
Cited by: 15
Author(s): Vineetha Vijayakumar, James Monypenny, Xing Judy Chen, Laura M. Machesky, Sérgio Lilla, Adrian J. Thrasher, Inés M. Antón, Yolanda Calle, Gareth E. Jones
Software Mentions: 2
Published: almost 13 years ago

10.1074/jbc.RA119.010486

Moonlighting matrix metalloproteinase substrates: Enhancement of proinflammatory functions of extracellular tyrosyl-tRNA synthetase upon cleavage
Cited by: 14
Author(s): Parker G. Jobin, Nestor Solis, Yoan Machado, Peter A. Bell, K. Simran, Nam Hoon Kwon, Sung Hoon Kim, Christopher M. Overall, Georgina S. Butler
Software Mentions: 2
Published: over 6 years ago

10.1074/jbc.M116.729806

Composition and Activity of the Non-canonical Gram-positive SecY2 Complex
Cited by: 8
Author(s): Mikaila Bandara, Robin A. Corey, Remy Martin, J. Mark Skehel, Ariel Blocker, Howard F. Jenkinson, Ian Collinson
Software Mentions: 2
Published: about 10 years ago

10.1186/1758-2946-5-5

Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines
Cited by: 23
Author(s): Sheng Tian, Youyong Li, Junmei Wang, Xiaojie Xu, Lei Xu, Xiaohong Wang, Lei Chen, Tingjun Hou
Software Mentions: 2
Published: over 13 years ago

10.1186/s13321-019-0391-2

Dataset’s chemical diversity limits the generalizability of machine learning predictions
Cited by: 59
Author(s): Marta Glavatskikh, Jules Leguy, Gilles Hunault, Thomas Cauchy, Benoit Da Mota
Software Mentions: 2
Published: almost 7 years ago

10.1074/jbc.RA119.012517

Phosphorylation of the overlooked tyrosine 310 regulates the structure, aggregation, and microtubule- and lipid-binding properties of Tau
Cited by: 27
Author(s): Nadine Ait-Bouziad, Anass Chiki, Galina Limorenko, Shifeng Xiao, David Eliezer, Hilal A. Lashuel
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1005640

Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum
Cited by: 71
Author(s): Sonia Campo, Kerrigan B. Gilbert, James C. Carrington
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-015-2262-1

Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea
Cited by: 13
Author(s): Kondethimmanahalli H. Chandramouli, Sarah Al-Aqeel, Taewoo Ryu, Huoming Zhang, Loqmane Seridi, Yanal Ghosheh, Pei‐Yuan Qian, Timothy Ravasi
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.ppat.1006001

The Listeria monocytogenes PASTA Kinase PrkA and Its Substrate YvcK Are Required for Cell Wall Homeostasis, Metabolism, and Virulence
Cited by: 61
Author(s): Daniel A. Pensinger, Kyle Boldon, Grischa Y. Chen, William J.B. Vincent, Sherman Kyle, Min Xiong, Adam J. Schaenzer, Emily R. Forster, Jörn Coers, Rob Striker, John-Demian Sauer
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.ppat.1008917

Novel Babesia bovis exported proteins that modify properties of infected red blood cells
Cited by: 15
Author(s): Hassan Hakimi, Thomas J. Templeton, Minoru Sakaguchi, Junya Yamagishi, Shuichi Miyazaki, Kazuhide Yahata, Takayuki Uchihashi, Shin-ichiro Kawazu, O. Kaneko, Masahito Asada
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pbio.3000774

Cell–substrate adhesion drives Scar/WAVE activation and phosphorylation by a Ste20-family kinase, which controls pseudopod lifetime
Cited by: 24
Author(s): Shashi P. Singh, Peter A. Thomason, Sérgio Lilla, Matthias Schaks, Qian Tang, Bruce L. Goode, Laura M. Machesky, Klemens Rottner, Robert H. Insall
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1009351

A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum
Cited by: 19
Author(s): Jun Miao, Chengqi Wang, Amuza Byaruhanga Lucky, Xiaoying Liang, Hui Min, Swamy Rakesh Adapa, Rays H. Y. Jiang, Kami Kim, Liwang Cui
Software Mentions: 2
Published: about 5 years ago

10.3390/proteomes6040039

Exploring Morphine-Triggered PKC-Targets and Their Interaction with Signaling Pathways Leading to Pain via TrkA
Cited by: 12
Author(s): Darlene Aparecida Pena, Mariana Lemos Duarte, Dimitrius T. Pramio, Lakshmi A. Devi, Deborah Schechtman
Software Mentions: 2
Published: about 8 years ago

10.1128/IAI.00537-19

Proximity Labeling To Map Host-Pathogen Interactions at the Membrane of a Bacterium-Containing Vacuole in Chlamydia trachomatis-Infected Human Cells
Cited by: 21
Author(s): Macy G. Olson, Ray E. Widner, Lisa M. Jorgenson, Alyssa Lawrence, Dragana Lagundžin, Nicholas T. Woods, Scot P. Ouellette, Elizabeth A. Rucks
Software Mentions: 2
Published: almost 7 years ago

10.1007/s00726-021-03006-7

Gamma-gliadin specific celiac disease antibodies recognize p31-43 and p57-68 alpha gliadin peptides in deamidation related manner as a result of cross-reaction
Cited by: 7
Author(s): Ádám Diós, Rita Elek, Ildikò Szabó, Szilvia Horváth, Judit Gyimesi, Róbert Király, Katharina Werkstetter, Sibylle Koletzko, László Fésüs, Ilma Rita Korponay-Szabó
Software Mentions: 2
Published: over 5 years ago

10.1002/btpr.2978

Multiplexed clonality verification of cell lines for protein biologic production
Cited by: 4
Author(s): Sofie A. O’Brien, Juhi Ojha, Paul Y K Wu, Wei Shou Hu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-5817-8

Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi
Cited by: 16
Author(s): Mari Mäkinen, Jaana Kuuskeri, Pia Laine, Olli‐Pekka Smolander, Andriy Kovalchuk, Zhen Zeng, Fred O. Asiegbu, Lars Paulín, Petri Auvinen, Taina Lundell
Software Mentions: 2
Published: over 7 years ago

10.1038/hortres.2016.29

Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid
Cited by: 14
Author(s): Supakan Rattanakan, Iniga S. George, Paul A. Haynes, Grant R. Cramer
Software Mentions: 2
Published: over 10 years ago

10.1126/sciadv.abg4102

A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts
Cited by: 19
Author(s): Sergio A. Muñoz-Gómez, M. Kreutz, Sebastian Hess
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-S12-S2

Time-course human urine proteomics in space-flight simulation experiments
Cited by: 22
Author(s): Hans Binder, Henry Wirth, Arsen Arakelyan, Kathrin Lembcke, Evgeny S. Tiys, В. А. Иванисенко, Н. А. Колчанов, Alexey Kononikhin, Igor Popov, E. N. Nikolaev, Л. Х. Пастушкова, И. М. Ларина
Software Mentions: 2
Published: almost 12 years ago

10.1038/srep15443

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations
Cited by: 75
Author(s): Abdallah Abdallah, Grant A. Hill-Cawthorne, Thomas D. Otto, Francesc Español i Coll, José Afonso Guerra-Assunção, Ge Gao, Raeece Naeem, Hifzur Rahman Ansari, Tareq B. Malas, Sabir A. Adroub, Theo Verboom, Roy Ummels, Huoming Zhang, Aswini K. Panigrahi, Ruth McNerney, Roland Brosch, Taane G. Clark, Marcel A. Behr, Wilbert Bitter, Arnab Pain
Software Mentions: 2
Published: almost 11 years ago

10.3390/jcm10112446

Characteristics of the Urinary Proteome in Women with Overactive Bladder Syndrome: A Case-Control Study
Cited by: 1
Author(s): Marianne Koch, Pavel Lyatoshinsky, Goran Mitulović, Barbara Bodner‐Adler, Sören Lange, Engelbert Hanzal, Wolfgang Umek
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.506

Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis
Cited by: 48
Author(s): Chelsea Nicole Laatsch, Blythe Durbin‐Johnson, David M. Rocke, Sophie Mukwana, Abby B. Newland, Michael J. Flagler, Michael Davis, Richard A. Eigenheer, Brett S. Phinney, Robert H. Rice
Software Mentions: 2
Published: about 12 years ago

10.1186/s13075-019-1961-4

Proteomic and histopathological characterisation of sicca subjects and primary Sjögren’s syndrome patients reveals promising tear, saliva and extracellular vesicle disease biomarkers
Cited by: 58
Author(s): Lara A. Aqrawi, Hilde Kanli Galtung, Eduarda Guerreiro, Reidun Øvstebø, Bernd Thiede, Tor Paaske Utheim, Xiangjun Chen, Øygunn Aass Utheim, Øyvind Palm, Kathrine Skarstein, Janicke Liaaen Jensen
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-020-77346-x

Acute pathophysiological myocardial changes following intra-cardiac electrical shocks using a proteomic approach in a sheep model
Cited by: 4
Author(s): Alexandre Bodin, Valérie Labas, Arnaud Bisson, Ana-Paula Teixeira-Gomes, Hélène Blasco, Daniel Tomas, Lucie Combes‐Soia, Paulo Marcelo, Élodie Miquelestorena-Standley, Christophe Baron, Denis Angoulvant, Dominique Babuty, Nicolas Clémenty
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-016-0951-y

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Cited by: 65
Author(s): Song Gao, Denis Bertrand, Burton K. Chia, Niranjan Nagarajan
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-021-83395-7

A Casz1–NuRD complex regulates temporal identity transitions in neural progenitors
Cited by: 15
Author(s): Pierre Mattar, Christine Jolicoeur, Dang Thanh Chung, Sujay Shah, Brian S. Clark, Michel Cayouette
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.7352

Comprehensive map and functional annotation of the mouse white adipose tissue proteome
Cited by: 7
Author(s): Xiaonan Tang, Juan Li, Weigang Zhao, Hui Sun, Jing Li, Zhu-Fang She, Tao Yuan, Shuainan Liu, Quan Liu, Yong Fu, Wei Sun
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-021-89907-9

Continual proteomic divergence of HepG2 cells as a consequence of long-term spheroid culture
Cited by: 2
Author(s): Andrea Antonio Ellero, Iman van den Bout, Maré Vlok, Allan Duncan Cromarty, Tracey Hurrell
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-945

Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts
Cited by: 25
Author(s): Amanda M. Hulse‐Kemp, Hamid Ashrafi, Xiuting Zheng, Fei Wang, Kevin A. Hoegenauer, Andrea Maeda, Shanshan Yang, Kevin Stoffel, Marta Matvienko, Kimberly Clemons, Joshua A. Udall, Allen Van Deynze, Don C. Jones, David M. Stelly
Software Mentions: 2
Published: almost 12 years ago

10.1038/s41598-021-92931-4

Overlapping regions of Caf20 mediate its interactions with the mRNA-5′cap-binding protein eIF4E and with ribosomes
Cited by: 4
Author(s): Ebelechukwu C. Nwokoye, Eiman AlNaseem, Robert A. Crawford, Lydia M. Castelli, Martin D. Jennings, Christopher J. Kershaw, Graham D. Pavitt
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-021-07678-z

ddRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)
Cited by: 6
Author(s): Yan Ji, Gábor Vétek, Chandan Pal, Jinping Zhang, Rania Gmati, Qing-Hai Fan, Disna N. Gunawardana, Allan Burne, Diane Anderson, K. B. Rebijith, Sherly George, Péter Farkas, Dongmei Li
Software Mentions: 2
Published: over 5 years ago

10.3390/genes10090650

Affinity Purification of NF1 Protein–Protein Interactors Identifies Keratins and Neurofibromin Itself as Binding Partners
Cited by: 11
Author(s): Rachel M. Carnes, Robert A. Kesterson, Bruce R. Korf, James A. Mobley, Deeann Wallis
Software Mentions: 2
Published: about 7 years ago

10.1534/g3.115.017053

The Mosaic Mutants of Cucumber: A Method to Produce Knock-Downs of Mitochondrial Transcripts
Cited by: 9
Author(s): Angel R. Del Valle-Echevarria, Agnieszka Kiełkowska, Grzegorz Bartoszewski, Michael J. Havey
Software Mentions: 2
Published: over 11 years ago

10.1534/genetics.119.302851

Imipridone Anticancer Compounds Ectopically Activate the ClpP Protease and Represent a New Scaffold for Antibiotic Development
Cited by: 30
Author(s): Samuel Jacques, Almer M. van der Sloot, Caroline Huard, Jasmin Coulombe-Huntington, Sarah Tsao, Sylvain Tollis, Thierry Bertomeu, Elizabeth Culp, Daniel Pallant, Michael A. Cook, Éric Bonneil, Pierre Thibault, Gerard D. Wright, Mike Tyers
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-5981-x

Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits
Cited by: 14
Author(s): Jitao Li, Jianjian Lv, Ping Liu, Ping Chen, Jiajia Wang, Jian Li
Software Mentions: 2
Published: about 7 years ago

10.3389/fnsyn.2017.00013

Activity-Dependent Phosphorylation by CaMKIIδ Alters the Ca2+ Affinity of the Multi-C2-Domain Protein Otoferlin
Cited by: 12
Author(s): Sandra Meese, A. Cepeda, Felix Gahlen, Christopher M. Adams, Ralf Ficner, Anthony J. Ricci, Stefan Heller, Ellen Reisinger, Meike Herget
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-015-2076-1

Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitrite
Cited by: 31
Author(s): Wenxu Zheng, Dagmar H. Leary, Jinny Liu, Robert E. Settlage, Kenan P. Fears, Stella H. North, Anahita Mostaghim, Tara Essock‐Burns, Sarah E. Haynes, Kathryn J. Wahl, Christopher M. Spillmann
Software Mentions: 2
Published: almost 11 years ago

10.3389/fvets.2020.584948

Protein Cargo of Extracellular Vesicles From Bovine Follicular Fluid and Analysis of Their Origin From Different Ovarian Cells
Cited by: 19
Author(s): Svetlana Uzbekova, Carmen Almiñana, Valérie Labas, Ana-Paula Teixeira-Gomes, Lucie Combes‐Soia, Guillaume Tsikis, Anaïs Vitorino Carvalho, Rustem Uzbekov, Г. Н. Сингина
Software Mentions: 2
Published: almost 6 years ago

10.1186/gb-2012-13-2-r11

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells
Cited by: 54
Author(s): Najeeb U. Siddiqui, Xiao Li, Hua Luo, Angelo Karaiskakis, Huayun Hou, Thomas Kislinger, J. Timothy Westwood, Quaid Morris, Howard D. Lipshitz
Software Mentions: 2
Published: almost 15 years ago

10.1128/mSphere.00100-20

MAG2, a Toxoplasma gondii Bradyzoite Stage-Specific Cyst Matrix Protein
Cited by: 8
Author(s): Vincent Tu, Joshua Mayoral, Rama R. Yakubu, Tadakimi Tomita, Tatsuki Sugi, Bing Han, Tere Williams, Yanfen Ma, Louis M. Weiss
Software Mentions: 2
Published: over 6 years ago

10.1038/hortres.2014.39

Dynamic changes in the date palm fruit proteome during development and ripening
Cited by: 35
Author(s): Claudius Marondedze, Chris Gehring, Ludivine Thomas
Software Mentions: 2
Published: about 12 years ago

10.3389/fpls.2017.01292

Stress-Related Mitogen-Activated Protein Kinases Stimulate the Accumulation of Small Molecules and Proteins in Arabidopsis thaliana Root Exudates
Cited by: 13
Author(s): Nadine Strehmel, Wolfgang Hoehenwarter, Susann Mönchgesang, Petra Majovsky, Sylvia Krüger, Dierk Scheel, Justin Lee
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-019-6194-z

The olfactory secretome varies according to season in female sheep and goat
Cited by: 7
Author(s): P A Cann, Malika Chabi, Aliénor Delsart, Chrystelle Le Danvic, Jean‐Michel Saliou, Manon Chasles, Matthieu Keller, Patricia Nagnan‐Le Meillour
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.mbplus.2020.100027

Proteomic fingerprints of damage in extracellular matrix assemblies
Cited by: 18
Author(s): Alexander Eckersley, Matiss Ozols, Ronan O’Cualain, Emma-Jayne Keevill, April Foster, Suzanne M. Pilkington, David Knight, Christopher E.M. Griffiths, Rachel Watson, Michael J. Sherratt
Software Mentions: 2
Published: over 6 years ago

10.3389/fbioe.2020.00882

Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems
Cited by: 26
Author(s): K. M. Shakirova, Viktoriia Y. Ovchinnikova, Э. Б. Дашинимаев
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2407-11-368

Purine Nucleoside Phosphorylase mediated molecular chemotherapy and conventional chemotherapy: A tangible union against chemoresistant cancer
Cited by: 11
Author(s): Preetinder Singh, Swapna Joshi, Pamela J. Russell, Sham V. Nair, Aparajita Khatri
Software Mentions: 2
Published: about 15 years ago

10.3389/fpls.2020.01230

Big Genes, Small Effectors: Pea Aphid Cassette Effector Families Composed From Miniature Exons
Cited by: 6
Author(s): Matthew Dommel, Jong‐Nam Oh, José C. Huguet‐Tapia, Endrick Guy, Hélène Boulain, Akiko Sugio, M. Murugan, Fabrice Legeai, Michelle Heck, Charlotte M. Smith, Frank F. White
Software Mentions: 2
Published: about 6 years ago

10.1186/s13072-016-0087-z

Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers
Cited by: 23
Author(s): Jian Sun, Yilin Zhao, Rebecca McGreal, Yamit Cohen‐Tayar, Shira Rockowitz, Carola Wilczek, Ruth Ashery‐Padan, David Shechter, Deyou Zheng, Aleš Cvekl
Software Mentions: 2
Published: about 10 years ago

10.15252/embr.201744807

<scp>PAWS</scp> 1 controls Wnt signalling through association with casein kinase 1α
Cited by: 24
Author(s): Polyxeni Bozatzi, Kevin S. Dingwell, Kevin Z. L. Wu, Fay Cooper, Timothy D. Cummins, Luke D. Hutchinson, J. Vogt, Nicola T. Wood, Thomas Macartney, Joby Varghese, Robert Gourlay, David G. Campbell, James C. Smith, Gopal P. Sapkota
Software Mentions: 2
Published: over 8 years ago

10.1186/1477-5956-7-9

A novel approach to denoising ion trap tandem mass spectra
Cited by: 27
Author(s): Jiarui Ding, Jinhong Shi, Guy G. Poirier, Fang‐Xiang Wu
Software Mentions: 2
Published: over 17 years ago

10.1002/2211-5463.12997

Cystatin C regulates the cytotoxicity of infection‐induced endothelial‐derived β‐amyloid
Cited by: 2
Author(s): Ron Balczon, K. Adam Morrow, Silas J. Leavesley, C.M. Francis, T. Stevens, Ezinne Agwaramgbo, Christopher Williams, R.P. Stevens, Geri Langham, S.B. Voth, Eugene A. Cioffi, Susan E Weintraub, Troy Stevens
Software Mentions: 2
Published: almost 6 years ago

10.3390/mps3010015

A Fast and Accurate Method to Identify and Quantify Enzymes in Brush-Border Membranes: In Situ Hydrolysis Followed by Nano LC-MS/MS
Cited by: 7
Author(s): Antonio Brun, Melisa E Magallanes, Carlos Martı́nez del Rio, Gregory A. Barrett-Wilt, William H. Karasov, Enrique Caviedes‐Vidal
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2018.01882

Development of a Rapid in planta BioID System as a Probe for Plasma Membrane-Associated Immunity Proteins
Cited by: 37
Author(s): Brendon Conlan, Thomas Stoll, Jeffrey J. Gorman, Isabel M. L. Saur, John P. Rathjen
Software Mentions: 2
Published: almost 8 years ago

10.1093/bioinformatics/btaa288

HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C
Cited by: 11
Author(s): Ryo Nakabayashi, Shinichi Morishita
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-5750-x

Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps
Cited by: 14
Author(s): Alexander Capraro, Denis O’Meally, Shafagh A. Waters, Hardip R. Patel, Arthur Georges, Paul D. Waters
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pbio.3001081

Molecular characterization of the conoid complex in Toxoplasma reveals its conservation in all apicomplexans, including Plasmodium species
Cited by: 49
Author(s): Luděk Kořený, Mohammad Zeeshan, Konstantin Barylyuk, Eelco C. Tromer, Jolien J. E. van Hooff, Declan Brady, Huiling Ke, Sara Chelaghma, David J. P. Ferguson, Laura Eme, Rita Tewari, Ross F. Waller
Software Mentions: 2
Published: over 5 years ago

10.1016/j.bbapap.2013.04.004

A tutorial for software development in quantitative proteomics using PSI standard formats
Cited by: 5
Author(s): Faviel F. Gonzalez-Galarza, Da Qi, Jun Fan, Conrad Bessant, Andrew R. Jones
Software Mentions: 2
Published: almost 13 years ago

10.15252/embj.201798714

Evidence for the nuclear import of histones H3.1 and H4 as monomers
Cited by: 39
Author(s): Michael James Apta‐Smith, Juan R. Hernández-Fernaud, Andrew Bowman
Software Mentions: 2
Published: about 8 years ago

10.1093/database/bav056

Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications
Cited by: 24
Author(s): Tamás Hegedűs, Pururawa Mayank Chaubey, György Várady, Edit Szabó, Hajnalka Sarankó, Lia Hofstetter, Bernd Roschitzki, Bruno Stieger, Balázs Sarkadi
Software Mentions: 2
Published: over 11 years ago

10.1111/tpj.13743

Multiple marker abundance profiling: combining selected reaction monitoring and data‐dependent acquisition for rapid estimation of organelle abundance in subcellular samples
Cited by: 13
Author(s): Cornelia M. Hooper, Tim J. Stevens, Anna Maija Saukkonen, Ian Castleden, Pragya Singh, Gregory W. Mann, Bertrand Fabre, Jun Ito, Michael J. Deery, Kathryn S. Lilley, Young-Mo Kim, A. Harvey Millar, Joshua L. Heazlewood, Harriet T. Parsons
Software Mentions: 2
Published: almost 9 years ago

10.1242/dev.185421

Ykt6-dependent endosomal recycling is required for Wnt secretion in the <i>Drosophila</i> wing epithelium
Cited by: 13
Author(s): Karen Linnemannstöns, Leonie Witte, Pradhipa Karuna, Jeanette Clarissa Kittel, Adi Danieli, Denise Madeddu, Lena Nitsch, Mona Honemann‐Capito, Ferdi Grawe, Andreas Wodarz, Julia Christina Gross
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.dib.2020.106064

Tandem mass tagged dataset used to characterize muscle-specific proteome changes in beef during early postmortem period
Cited by: 2
Author(s): Chaoyu Zhai, B. A. Djimsa, Kitty Brown, Jessica E. Prenni, D. R. Woerner, K. E. Belk, Mahesh N. Nair
Software Mentions: 2
Published: about 6 years ago

10.1038/s42003-021-02214-x

Placental secretome characterization identifies candidates for pregnancy complications
Cited by: 16
Author(s): Tina Napso, Xiaohui Zhao, Marta Ibañez-Lligoña, Ionel Sandovici, Richard G. Kay, Amy L. George, Fiona M. Gribble, Frank Reimann, Claire L Meek, Russell S. Hamilton, Amanda N. Sferruzzi‐Perri
Software Mentions: 2
Published: over 5 years ago

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